Eye in a Disk: eyeIntegration human pan-eye and body transcriptome database version 1.0

Swamy, Vinay; McGaughey, David

doi:10.1101/579482

Cited by 9 publications

(13 citation statements)

References 69 publications

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“…Recently, TRPM3 has been immuno-localized to subdomains of the apical plasma membrane of human fetal RPE cells with particular enrichment at apical tight junctions and the base of primary cilia [136]. RNA sequencing confirms that TRPM3 is more abundant in human RPE tissue and cell lines and a lens stem cell line than in retinal or corneal derived cells [137,138].…”

Section: Human Trpm3_mir204mentioning

confidence: 95%

TRPM3_miR-204: a complex locus for eye development and disease

Shiels

2020

Hum Genomics

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First discovered in a light-sensitive retinal mutant of Drosophila, the transient receptor potential (TRP) superfamily of non-selective cation channels serve as polymodal cellular sensors that participate in diverse physiological processes across the animal kingdom including the perception of light, temperature, pressure, and pain. TRPM3 belongs to the melastatin sub-family of TRP channels and has been shown to function as a spontaneous calcium channel, with permeability to other cations influenced by alternative splicing and/or non-canonical channel activity. Activators of TRPM3 channels include the neurosteroid pregnenolone sulfate, calmodulin, phosphoinositides, and heat, whereas inhibitors include certain drugs, plant-derived metabolites, and G-protein subunits. Activation of TRPM3 channels at the cell membrane elicits a signal transduction cascade of mitogen-activated kinases and stimulus response transcription factors. The mammalian TRPM3 gene hosts a non-coding microRNA gene specifying miR-204 that serves as both a tumor suppressor and a negative regulator of post-transcriptional gene expression during eye development in vertebrates. Ocular co-expression of TRPM3 and miR-204 is upregulated by the paired box 6 transcription factor (PAX6) and mutations in all three corresponding genes underlie inherited forms of eye disease in humans including early-onset cataract, retinal dystrophy, and coloboma. This review outlines the genomic and functional complexity of the TRPM3_miR-204 locus in mammalian eye development and disease.

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Section: Human Trpm3_mir204mentioning

confidence: 95%

TRPM3_miR-204: a complex locus for eye development and disease

Shiels

2020

Hum Genomics

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“…Retrieved datasets from Eyeintegration database. 45,46 results indicated that CE cells decreased LIN28 expression during development and despite the low transcriptional and protein levels, newborn CE cells still retain a vestige of LIN28 expression.…”

Section: Lin28 and Hmga2 Expression In Ce Cellsmentioning

confidence: 96%

“…EyeIntegration transcriptome database is available in the public domain at https://eyeIntegration.nei.nih.gov. 45,46 Human adult and fetal retina datasets were collected from SRP080002, 47 SRP080886, 48 SRP098761, 49 SRP015336, 50 SRP034875, 49 SRP105756, 51 SRP090040, 52 and SRP119766. 53 Adult retinal pigmented epithelium (RPE)-and embryonic stem cell (ESC)-derived RPE datasets were collected from the SRP064956, 54 SRP070938, 55 SRP062870, 56 SRP091675, 57 SRP094572, 58 SRP110135, 59 and SRP011895.…”

Section: Gene Expression Datasetsmentioning

confidence: 99%

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Let-7, Lin28 and Hmga2 Expression in Ciliary Epithelium and Retinal Progenitor Cells

Frasson

Dalmaso

Akamine

et al. 2021

Invest. Ophthalmol. Vis. Sci.

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Purpose Ciliary epithelium (CE) of adult mammalian eyes contains quiescent retinal progenitor/stem cells that generate neurospheres in vitro and differentiate into retinal neurons. This ability doesn't evolve efficiently probably because of regulatory mechanisms, such as microRNAs (miRNAs) that control pluripotent, progenitor, and differentiation genes. Here we investigate the presence of Let-7 miRNAs and its regulator and target, Lin28 and Hmga2, in CE cells from neurospheres, newborns, and adult tissues. Methods Newborn and adult rats CE cells were dissected into pigmented and nonpigmented epithelium (PE and NPE). Newborn PE cells were cultured with growth factors to form neurospheres and we analyzed Let-7 , Lin28a, and Hmga2 expression. During the neurospheres formation, we added chemically modified single-stranded oligonucleotides designed to bind and inhibit or mimic endogenous mature Let-7 b and Let-7 c. After seven days in culture, we analyzed neurospheres size, number and expression of Let-7 , Lin28, and Hmga2. Results Let-7 miRNAs were expressed at low rates in newborn CE cells with significant increase in adult tissues, with higher levels on NPE cells, that does not present the stem cells reprogramming ability. The Lin28a and Hmga2 protein and transcripts were more expressed in newborns than adults cells, opposed to Let-7 . Neurospheres presented higher Lin28 and Hmga2 expression than newborn and adult, but similar Let-7 than newborns. Let-7 b inhibitor upregulated Hmga2 expression, whereas Let-7 c mimics upregulated Lin28 and downregulated Hmga2 . Conclusions This study shows the dynamic of Lin28- Let-7 -Hmga regulatory axis in CE cells. These components may develop different roles during neurospheres formation and postnatal CE cells.

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The Human Eye Transcriptome Atlas: A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue

Wolf

Boneva

Schlecht

et al. 2021

Preprint

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The applications of deep sequencing technologies in life science research and clinical diagnostics have increased rapidly over the last decade. Although fast algorithms for data processing exist, intuitive, portable solutions for data analysis are still rare. For this purpose, we developed a web-based transcriptome database, which provides a platform-independent, intuitive solution to easily explore and compare ocular gene expression of 100 diseased and healthy human tissue samples from 15 different tissue types collected at the Eye Center of the University of Freiburg. To ensure comparability of expression between different tissues, reads were normalized across all 100 samples. Differentially expressed genes were calculated between each tissue type to determine tissue-specific genes. Unsupervised analysis of all 100 samples revealed an accurate clustering according to different tissue types. Cluster analysis based on known cell type-specific marker genes allowed differentiation of respective tissues. Several tissue-specific marker genes were identified. These genes were involved in tissue- or disease-specific processes, such as myelination for the optic nerve, visual perception for retina, keratinocyte differentiation for conjunctival carcinoma, as well as endothelial cell migration for choroidal neovascularization membranes. The results are accessible at the Human Eye Transcriptome Atlas website at https://www.eye-transcriptome.com. In summary, this searchable transcriptome database enables easy exploration of ocular gene expression in healthy and diseased human ocular tissues without bioinformatics expertise. Thus, it provides rapid access to detailed insights into the molecular mechanisms of various ocular tissues and diseases, as well as the rapid retrieval of potential new diagnostic and therapeutic targets.

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Eye in a Disk: eyeIntegration human pan-eye and body transcriptome database version 1.0

Cited by 9 publications

References 69 publications

TRPM3_miR-204: a complex locus for eye development and disease

TRPM3_miR-204: a complex locus for eye development and disease

Let-7, Lin28 and Hmga2 Expression in Ciliary Epithelium and Retinal Progenitor Cells

The Human Eye Transcriptome Atlas: A Searchable Comparative Transcriptome Database for Healthy and Diseased Human Eye Tissue

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